> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/icm/analyses/analysis-functionality/task-menu/biological-interpretation/correlation-engine-atlases.md).

# Correlation Engine atlases

The **Correlation Engine atlases** task is a biological interpretation tool that queries your differential analysis results against a set of atlases, enabling biological insights across multiple contexts. In Connected Multiomics, the **Correlation Engine atlases** task supports four atlases:

* *Body atlas*: queries for tissue, cell type, single cell relevant to your genes.
* *Disease atlas*: queries for diseases, traits, conditions, and surrogate endpoints associated with a gene.
* *Knockdown atlas*: queries for genetic perturbations (knockdown, knockout, or overexpression) affecting your gene, and how.
* *Pharmaco atlas*: queries for compounds and treatments significantly correlated to a gene, sequence region, biogroup, or bioset.

## Invoking Correlation Engine atlases

The **Correlation Engine atlases** task can be invoked from a differential analysis data node or a filtered feature list (e.g., filtered differential analysis result).

* Select a differential analysis data node or a filtered feature list data node.
* Under **Biological interpretation** menu section, select **Correlation Engine atlases**.
* Choose **Organism**, **Correlation Engine project**, and give a **name** to the Correlation Engine study, then click **Next**.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-5db32e3b223214d17b5f2465505fe893141dd34d%2FCEA_setUp_pg1.png?alt=media" alt=""><figcaption></figcaption></figure>

* Select a **Contrast** for the Correlation Engine analysis, choose a **feature identifier**, then click **Finish** to run the analysis.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-2d74f25e166e1d4a4a4ebb3c1ab0b01001ac98f2%2FCEA_setUp_pg2.png?alt=media" alt="" width="428"><figcaption></figcaption></figure>

## Correlation Engine atlases report

The Correlation Engine atlases task produces a task node and four data nodes - one for each atlas. Double-click on an atlas data node to view report.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-6288838123a71bd8bd13e654e13f598cd793b4ef%2Fcea_task_graph.png?alt=media" alt="" width="322"><figcaption></figcaption></figure>

Atlas report opens into a data viewer with one or more result sheets, depending on the atlas. Each result sheet consists of a result table and a bar chart colored to reflect direction of regulation (blue for up, red for down). An example of knockdown atlas report is shown below, consisting of four result sheets, each for a different genetic perturbation.

<figure><img src="https://580316046-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FWMxqQAMFOJtu98OBk9KN%2Fuploads%2Fgit-blob-d654faf2a973085d20e82a235dd4c2d93b20ff50%2Fcea_knockdown_atlas.png?alt=media" alt=""><figcaption></figcaption></figure>

## Reference

1. Kupershmidt I, Su QJ, Grewal A, Sundaresh S, Halperin I, Flynn J, et al. (2010) Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data. PLoS ONE 5(9): e13066.


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